A Mystery At The Heart of Life
(Revised from an article published in the online magazine Behemoth)
Ann Gauger
Our bodies are made up of cells, some 100 trillion of them. From biology class in high school or college, you remember some of their basic structures, like the nucleus at the center. We tend to think of cells as static, frozen, because that’s how they were presented to us on the page of a textbook. In fact, the cell is like the most antic, madcap, crowded yet fantastically efficient city you could ever picture. And at its heart lies a mystery—an essential set of mutually interdependent processes without which life would not be possible.
To tell this story we have to begin with the nucleus of the cell, where the cell’s information storage system resides. The nucleus is something like the cell’s Grand Central Library, where permanent instructions for how to make every protein the cell needs are stored. The medium on which the information is stored is DNA, a molecule made up of two long strings of atoms that are wound around each other in that famous double helix you may have seen pictures of. When I say long strings of atoms, I mean long. If all the DNA in one of your cells was written out in 12-point font it would stretch from Thunder Bay, Ontario to Hawaii.
Let’s continue the metaphor. If DNA is like a library, then chromosomes are like vast sections of the library. You have two sets of chromosomes, making a total of 46 altogether. In each chromosome, large portions of the DNA are very tightly supercoiled and packed against the nuclear wall, inactive, like books that have been stored in deep archives.
Nearer the center, active sections of each chromosome occupy certain regions, like books in the library stacks. In the very center, unwound loops of DNA (the books that are actually being read) partner with other loops in an intricate collaboration. But DNA doesn’t do the mediating and collaborating. Instead, swarming about the DNA strands are clouds of signaling molecules, proteins that bind to the signaling molecules, and still other proteins that bind to them both and to the DNA itself in a sort of sandwich arrangement.
This baroque cascade of interactions between signals, proteins, and DNA determines which genes will be turned on and which will be turned off. If the right combinations of molecules and binding proteins attach to the DNA in the right locations (the right kind of sandwiches are made), the neighboring genes will be activated for transcription.
Here’s what transcription means. A very particular binding protein made just for a particular DNA sequence, which has been drifting around waiting for the signal to bind, sits down on its particular sequence like a rider in a saddle, right in front of a particular gene. This protein changes its shape because it has bound DNA. In its new shape, it begins to bind other proteins, one by one. When this cluster of proteins gets large enough—all connected to the DNA—the cluster attracts one specialized kind of protein called an RNA polymerase.
Everything is nearly ready now. The whole complex of proteins waits like a racehorse in the starting gate until the signal is given, then bang! The polymerase takes off, leaving the other proteins behind, and starts copying DNA into RNA at an astonishing clip of 30 nucleotides per second. To give you an idea how fast this is, a professional typist can type on the order of 330 characters per minute, or about 5.5 characters per second. The polymerase is six times faster. We call this process transcription.
Sometimes the polymerase jumps between strands of DNA, forming an RNA copied from sections of two separate chromosomes. Sometimes polymerases racing in opposite directions run into each other, like Keystone cops. And sometimes polymerases run into places where DNA is being duplicated in order for the cell to divide. The RNA polymerase politely steps aside.
As it travels, this enzyme and its helper proteins literally unzip the double-stranded DNA and make a copy of one part of one strand (one gene).
There is another important process called replication, which uses a different protein called DNA polymerase to copy the DNA double helix, making two double helixes. The DNA has been faithfully replicated. Sounds simple, right? No. I left out some important bits.
To replicate DNA, a protein called a helicase unwinds the DNA, creating a fork with two strands. The two strands of the DNA are anti-parallel--they run in opposite directions. One DNA polymerase duplicates the right strand of the DNA. Another protein casts off loops of DNA on the left strand so it can be copied in the opposite direction. Meanwhile, thirty or so other proteins keep watch over the DNA, proofreading, correcting, and ensuring very few errors occur— about 1 mistake per billion nucleotides copied.
Both transcription and replication take place in the nucleus, where the DNA is.
Then the RNA gets processed and shipped out to the cytoplasm (the cytoplasm is everything in the cell outside of the nucleus) where most of the action of the cell takes place. There, the RNA is turned into proteins, including all those proteins necessary for DNA regulation. This process is called translation, because the RNA nucleotides get translated into amino acids, and the amino acids are strung together to make proteins. Translation takes place in molecular machines called ribosomes. Transcription and translation are necessary to make all the thousands of other proteins the cell requires. Proteins are the actors that accomplish things in the cell and are the building blocks that contribute to cellular architecture. So the cell has lots of ribosomes, and more must be made each time the cell divides into two cells.
Ribosomes are indispensable, efficient, self-correcting, decoding machines and protein factories. They are made of many ribosome-specific proteins woven together with several ribosomal RNAs in tangled knots that somehow work together. Deciphering the shape of the ribosome won three scientists the 2009 Nobel Prize for Chemistry.
Out in the cytoplasm messenger RNA finds a ribosome and feeds through it like ticker tape. The ribosome reads the message and translates it into amino acids and then stitches together the amino acids to make a protein. (That went by fast! I skipped way too much really interesting stuff.)
Though not as fast as transcription, the ribosome manages a respectable rate of 6 to 9 amino acids per second, a little faster than the best of our typists. But consider this-- there are 20+ amino acids for the ribosome to sort through in order to find the right one for each nucleotide to be translated. I imagine the scene to be like Aunt Wilma rummaging through a pile of stuff, and tossing out items, saying, “No, not this one, not that one, not this one, no , no, ah, yes! this fits!” and click, the amino acid slides into place. Given that kind of search process, 6 to 9 amino acids per second become a ticker tape on fast forward.
There is much more to this story than I have time to tell — suffice it to say that the genetic code, its replication, transcription, and translation, are at the center of life: They are interdependent highly optimized processes that are essential to life. And at the very center of these processes essential to life is this mystery: which came first, the protein, RNA, or the DNA? And how was the link between DNA and protein established? If we are supposed to have evolved by the gradual accretion of molecules that somehow turn into DNA and protein
A favored hypothesis is that RNA came first. But there are problems with this theory because RNA can only weakly copy a small portion of its sequence if provided with everything it needs by the researcher; it is unlikely to be able to carry out all the many chemical activities required by the cell.
We may someday figure out some of these relationships. As is the nature of things, more mysteries will be revealed when we do. In fact, it may well be that at the very center of life, of existence itself, there lies a mystery known only to God. In the meantime, though, it is He who has given us the ability and desire to search out the truth of things. For as Proverbs 25:2 says, “It is the glory of God to conceal a matter; to search out a matter is the glory of kings.”